An RNA-Seq data exploration tool that shows read map coverage of a gene of interest along with a coloured "electronic fluorescent pictographic" (eFP) based on its RPKM expression level.
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Apr 8, 2024 - HTML
An RNA-Seq data exploration tool that shows read map coverage of a gene of interest along with a coloured "electronic fluorescent pictographic" (eFP) based on its RPKM expression level.
SPIRO is a Smart Plate Imaging Robot
A simple python library to identify the most likely strain from the population
Interactive Functional Annotations Dashboard
🌱🧬 Collection of scripts for the paper: "PAMP-triggered genetic reprogramming involves widespread alternative transcription initiation and an immediate transcription factor wave" (The Plant Cell 2022; PMID 35404429 🔗)
Nextflow pipeline for SNPmatch (https://github.com/Gregor-Mendel-Institute/SNPmatch.git)
Arabidopsis EcoGEx (R-📦 + 🕸️-App)
HiFi-SR is a Python-based pipeline for the detection of plant mitochondrial structural rearrangements based on the mapping of PacBio high-fidelity (HiFi) reads or Circular Consensus Sequencing (ccs) data, to a reference genome (i.e., the hypothetical master cycle DNA).
A website to explore biological relationships between Arabidopsis thailiana genetic characteristics.
Analysis of transcriptomic dataset of A. thaliana Multi Protein Bridging Factor 1c knockout
Gene ID Retrieval from TAIR: R code to retrieve gene IDs from TAIR (The Arabidopsis Information Resource) and export them as CSV files
Clustering of 1,135 Arabidopsis thaliana genomes from 1001 Genomes Project (https://1001genomes.org/)
🌱🧬 Collection of scripts for the paper: 📑 "Characterization of Arabidopsis thaliana Promoter Bidirectionality and Antisense RNAs by Inactivation of Nuclear RNA Decay Pathways" (The Plant Cell 2020; PMID 32213639 🔗)
An automated pipeline for analyzing arabidopsis luciferase imaging data
Regularly updated version of `org.At.tair.db`.
arabidopsis-maf-cap-accessions. genome extraction, alignments, visualization, phylogenomics, ancestral tree
Genomic prediction of amino acid traits in Arabidopsis seeds
Nextflow pipeline to assemble genomes from nanopore reads.
Anlysis of small RNAs in Arabidopsis SWR1 mutant (published in Choi et al. 2016, Plant Physiology, http://www.plantphysiol.org/content/171/2/1128)
A pipeline to analyse small RNA expression using Illumina sequencing data
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